Merge pull request #10 from jluethi/2_tests_for_2d_to_3d

Add coverage to CI

.github/workflows/ci_pip.yml

@@ -30,7 +30,7 @@ jobs:
           cache: "pip"
 
       - name: Install package
-        run: python -m pip install .[dev,test]
+        run: python -m pip install -e .[dev,test]
 
       - name: Install some testing dependencies (hard-coded)
         run: python -m pip install pytest devtools jsonschema requests wget pooch
@@ -46,7 +46,7 @@ jobs:
         run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing -s --log-cli-level debug
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4.0.1
+        uses: codecov/codecov-action@v4.3.1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           slug: jluethi/fractal-helper-tasks

README.md

@@ -1,5 +1,10 @@
 # fractal-helper-tasks
 
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](LICENSE)
+![Python version](https://img.shields.io/badge/python-%3E%3D3.9-blue)
+![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/jluethi/fractal-helper-tasks/your-workflow-file.yml?branch=main)
+[![codecov](https://codecov.io/gh/jluethi/fractal-helper-tasks/graph/badge.svg?token=ednmg2GzOw)](https://codecov.io/gh/jluethi/fractal-helper-tasks)
+
 Collection of Fractal helper tasks
 
 ## Development instructions

pyproject.toml

@@ -69,7 +69,13 @@ extend-ignore = [
 "tests/*.py" = ["D", "S"]
 "setup.py" = ["D"]
 
-[tool.deptry]
-exclude = [
-  'tests', 'examples'
+[tool.coverage.run]
+# Include only the specific package directories for coverage, exclude tests
+include = [
+    "src/fractal_helper_tasks/*"
+]
+omit = [
+    "*/tests/*",
+    "*_test.py",
+    "setup.py"
 ]

tests/conftest.py

@@ -53,7 +53,6 @@ def zenodo_zarr(testdata_path: Path) -> list[str]:
             f"{file_name}.zip", processor=pooch.Unzip(extract_dir=file_name)
         )
         zarr_full_path = file_paths[0].split(file_name)[0] + file_name
-        print(zarr_full_path)
         folder = folders[ind]
 
         # 2) Copy the downloaded Zarr into tests/data

tests/test_convert_2d_to_3d_segmentation.py

@@ -1,22 +1,29 @@
 """Test copy 2D to 3D segmentation."""
 
 import dask.array as da
+import pytest
 import zarr
 
 from fractal_helper_tasks.convert_2D_segmentation_to_3D import (
     convert_2D_segmentation_to_3D,
 )
 
 
-def test_2d_to_3d(tmp_zenodo_zarr: list[str]):
+@pytest.mark.parametrize("new_label_name", [None, "nuclei_new"])
+def test_2d_to_3d(tmp_zenodo_zarr: list[str], new_label_name):
     zarr_url = f"{tmp_zenodo_zarr[1]}/B/03/0"
     label_name = "nuclei"
 
     convert_2D_segmentation_to_3D(
         zarr_url=zarr_url,
         label_name=label_name,
+        new_label_name=new_label_name,
     )
-    zarr_3D_label_url = f"{tmp_zenodo_zarr[0]}/B/03/0/labels/{label_name}"
+
+    if not new_label_name:
+        new_label_name = label_name
+
+    zarr_3D_label_url = f"{tmp_zenodo_zarr[0]}/B/03/0/labels/{new_label_name}"
     # Check that the label has been copied correctly
     with zarr.open(zarr_3D_label_url, mode="rw+") as zarr_img:
         zarr_3D = da.from_zarr(zarr_img[0])
@@ -25,7 +32,9 @@ def test_2d_to_3d(tmp_zenodo_zarr: list[str]):
 
 # TODO: Add custom ROI tables to be copied to 3D
 
-# TODO: Add test with new label name, new table names
+# TODO: Add a feature table & have it copied over
+
+# TODO: Add test with new table names
 
 # TODO: Create a version of the test data where image suffixes need to be
 # changed, run tests on those